{"id":"https://openalex.org/W4417277204","doi":"https://doi.org/10.1093/bib/bbaf631.049","title":"Nativeness-constrained diffusion framework for nanobody design","display_name":"Nativeness-constrained diffusion framework for nanobody design","publication_year":2025,"publication_date":"2025-12-01","ids":{"openalex":"https://openalex.org/W4417277204","doi":"https://doi.org/10.1093/bib/bbaf631.049"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf631.049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf631.049","pdf_url":"https://academic.oup.com/bib/article-pdf/26/Supplement_1/i31/65854423/bbaf631.049.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/Supplement_1/i31/65854423/bbaf631.049.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109293273","display_name":"Yinghan Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Yinghan Zhang","raw_affiliation_strings":["Department of Surgery, The Chinese University of Hong Kong ,","Department of Surgery, The Chinese University of Hong Kong, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Surgery, The Chinese University of Hong Kong ,","institution_ids":["https://openalex.org/I177725633"]},{"raw_affiliation_string":"Department of Surgery, The Chinese University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054551177","display_name":"Tao Jiang","orcid":"https://orcid.org/0000-0003-0419-7288"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Tao Jiang","raw_affiliation_strings":["Department of Surgery, The Chinese University of Hong Kong ,","Department of Surgery, The Chinese University of Hong Kong, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Surgery, The Chinese University of Hong Kong ,","institution_ids":["https://openalex.org/I177725633"]},{"raw_affiliation_string":"Department of Surgery, The Chinese University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062712619","display_name":"Cheuk Shuen Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100303","display_name":"Biotech Park","ror":"https://ror.org/00mv0vt78","country_code":"IN","type":"government","lineage":["https://openalex.org/I4210100303"]},{"id":"https://openalex.org/I70986742","display_name":"Novelis (Canada)","ror":"https://ror.org/03wn09h25","country_code":"CA","type":"company","lineage":["https://openalex.org/I70986742"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CA","HK","IN"],"is_corresponding":false,"raw_author_name":"Cheuk Shuen Li","raw_affiliation_strings":["Saint Novel Biotech Limited ,","University of Hong Kong ,","University of Hong Kong, Hong Kong","Saint Novel Biotech Limited, Hong Kong"],"affiliations":[{"raw_affiliation_string":"Saint Novel Biotech Limited ,","institution_ids":["https://openalex.org/I4210100303"]},{"raw_affiliation_string":"University of Hong Kong ,","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"Saint Novel Biotech Limited, Hong Kong","institution_ids":["https://openalex.org/I70986742"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5109293273"],"corresponding_institution_ids":["https://openalex.org/I177725633"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.56357174,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"Supplement_1","first_page":"i31","last_page":"i31"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9861999750137329,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9861999750137329,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.004999999888241291,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.00279999990016222,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.49779999256134033},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.4302000105381012},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.42989999055862427},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.35409998893737793},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.31470000743865967},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.290800005197525}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.571399986743927},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.49779999256134033},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46970000863075256},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.4302000105381012},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.42989999055862427},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.35409998893737793},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32739999890327454},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32199999690055847},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.31470000743865967},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.30059999227523804},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.290800005197525},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.2896000146865845},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.27469998598098755},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.2581000030040741},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25200000405311584}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaf631.049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf631.049","pdf_url":"https://academic.oup.com/bib/article-pdf/26/Supplement_1/i31/65854423/bbaf631.049.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12699649","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12699649/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12699649/pdf/bbaf631.049.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf631.049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf631.049","pdf_url":"https://academic.oup.com/bib/article-pdf/26/Supplement_1/i31/65854423/bbaf631.049.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4417277204.pdf","grobid_xml":"https://content.openalex.org/works/W4417277204.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Abstract":[0],"Aim":[1],"Nanobodies":[2],"are":[3,65],"single-domain":[4,203],"antibodies":[5],"with":[6,91,138],"promising":[7],"therapeutic":[8],"potential,":[9],"yet":[10],"accurate":[11,198],"complementarity-determining":[12],"region":[13],"(CDR)":[14],"design":[15,135,201],"remains":[16],"challenging.":[17],"Methods":[18],"Existing":[19],"diffusion-based":[20,139],"frameworks":[21],"such":[22],"as":[23],"DiffAb[1]":[24],"and":[25,37,99,115,136],"RFantibody[2]":[26],"typically":[27],"generate":[28],"CDR":[29],"sequences":[30,63],"on":[31],"fixed":[32],"scaffolds":[33],"by":[34],"enforcing":[35],"structural":[36],"physical":[38,89],"constraints,":[39],"but":[40,70],"they":[41],"neglect":[42],"evolutionary":[43],"information":[44],"intrinsic":[45],"to":[46],"antibody":[47,110,134],"repertoires.":[48],"We":[49],"propose":[50],"a":[51,57,105],"scaffold-constrained":[52],"diffusion":[53],"framework":[54],"that":[55,64,86],"integrates":[56],"nativeness":[58],"prior,":[59],"guiding":[60],"generation":[61],"toward":[62],"not":[66],"only":[67],"structurally":[68],"consistent":[69],"also":[71],"evolutionarily":[72],"plausible.":[73],"Results":[74],"By":[75],"incorporating":[76],"nativeness-aware":[77],"constraints":[78],"during":[79],"design,":[80],"our":[81],"model":[82],"produces":[83],"nanobody":[84,117],"candidates":[85],"better":[87],"balance":[88],"compatibility":[90],"natural":[92],"repertoire":[93],"characteristics,":[94],"achieving":[95],"improved":[96],"sequence":[97],"realism":[98],"developability.":[100],"Conclusion":[101],"This":[102],"approach":[103],"provides":[104],"new":[106],"computational":[107],"strategy":[108],"for":[109,142],"engineering,":[111],"enabling":[112],"more":[113],"realistic":[114],"efficient":[116],"design.":[118],"References":[119],"1.":[120],"Luo":[121],"S.,":[122,128,192,194],"Su":[123],"Y.,":[124],"Peng":[125,129],"X.,":[126],"Wang":[127],"J.,":[130],"Ma":[131],"J.":[132],"\u2018Antigen-specific":[133],"optimization":[137],"generative":[140],"models":[141],"protein":[143],"structures.\u2019":[144],"Advances":[145],"in":[146],"Neural":[147],"Information":[148],"Processing":[149],"Systems":[150],"2022.":[151],"2.":[152],"Bennett":[153],"N.R.,":[154],"Watson":[155],"J.L.,":[156],"Ragotte":[157],"R.J.,":[158],"Borst":[159],"A.J.,":[160],"See":[161],"D.L.,":[162],"Weidle":[163],"C.,":[164,182],"Biswas":[165],"R.,":[166,176],"Shrock":[167],"E.L.,":[168],"Leung":[169],"P.J.Y.,":[170],"Huang":[171],"B.,":[172,180],"Goreshnik":[173],"I.,":[174],"Ault":[175],"Carr":[177],"K.D.,":[178],"Singer":[179],"Criswell":[181],"Vafeados":[183],"D.,":[184],"Garcia":[185],"Sanchez":[186],"M.,":[187],"Kim":[188],"H.M.,":[189],"V\u00e1zquez":[190],"Torres":[191],"Chan":[193],"Baker":[195],"D.":[196],"\u2018Atomically":[197],"de":[199],"novo":[200],"of":[202],"antibodies.\u2019":[204],"bioRxiv":[205],"2024.":[206]},"counts_by_year":[],"updated_date":"2026-03-10T14:07:55.174380","created_date":"2025-12-12T00:00:00"}